Dear all,
I performed simple simulations of TIP4P-Ew water for 500 ps with three
different GROMACS versions, namly 3.2.1, 3.3.1 and 4.0.2. There are 1000
molecules in the box and the temperature was 303 K at 1 bar. When I
compare the total energies of the three equilibrated simulations I get:
Hi
I want to do MD with a protien with prydoxal phosphate(PLP) which attache
covalently to one lysine.
For this I extract the Toplogy of lysine-PLP from PRODRG server.(DRGGMX.ITP
and DRGPOH.PDB).I Changed the name DRGGMX.ITP to DRG.itp.
after donig
pdb2gmx -f m.pdb -o m1.pdb -water spce with
Dear All,
This has been discussed before for individual frames. But I am having a
problem in trying to center a trajectory so that the bilayer remains at the
center of the box. I have tried several combinations, but none of the them
work. In each case, the centering and/or the fitting is done on
What is the problem exactly? The two layers separate over the pbc?
did you try a -pbc nojump prior the centering?
On Jul 3, 2009, at 11:37 AM, maria goranovic wrote:
Dear All,
This has been discussed before for individual frames. But I am
having a problem in trying to center a trajectory
Hi haziz...@razi.tums.ac.ir,
I think it's better to only use PRODRG for the pyridoxal phosphate
part. Then you can process the rest of the protein as usual,
preserving the parameters for lysine backbone and side chain. The PLP
part you can renumber and merge with the protein topology, adding
hi i'm simulating a ion channel protein in DPPC membrane. i'm following
Justin's tutorial for that. and have completed upto the solvation step. but
right after solvation, i found some water molecules in the channel. now i want
to delete those molecules. in the tutorial it is advised tyo use the
Hi,
I would say that those are water molecule which enter from the bulk
water. This is normal and probably important for the physiological
function of the system.
Best,
Itamar
On Fri, Jul 3, 2009 at 8:08 PM, Samik Bhattacharyasamikb...@yahoo.co.in wrote:
hi i'm simulating a ion channel protein
Well the bilayer drifts down in the z-direction, and eventually the leaflets
almost separate, with each leaflet being on opposite ends of the box.
if i try pbc nojump, the lipids drift far away from the box in the xy plane
On Fri, Jul 3, 2009 at 12:00 PM, gmx-users-requ...@gromacs.org wrote:
This sounds pretty bad! You have a drift of your all system
apparently ...
Did you not remove the COM of your system?
For membranes it is often recommended to remove the water and the
lipid bilayer separately. The might drift one from the other.
On Jul 3, 2009, at 12:19 PM, maria goranovic
--- On Fri, 3/7/09, Itamar Kass itamar.k...@gmail.com wrote:
From: Itamar Kass itamar.k...@gmail.com
Subject: Re: [gmx-users] waters in ion channels
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Friday, 3 July, 2009, 3:42 PM
Hi,
I would say that those are water molecule
:
http://lists.gromacs.org/pipermail/gmx-users/attachments/20090703/266f5139/attachment-0001.html
--
Message: 3
Date: Fri, 3 Jul 2009 20:12:37 +1000
From: Itamar Kass itamar.k...@gmail.com
Subject: Re: [gmx-users] waters in ion channels
To: Discussion list
Hello,
If you simply need to remove water molecules, you can simply use VMD,
Pymol or whatever allows you to select and save atom coordinates in a
format readable by gromacs. In VMD, I would do something like:
set sel [atomselect top not (same resid as (water within 5 of
resname DPPC)]
or
Hello Xavier, and sorry to bump in. I am also having that same issue just as
Maria described - could you please explain in a bit more details why does
that happen?
I mean, why does the membrane move along z-axis, and how to solve/avoid it?
Thanks a lot,
-Shay
_
From:
I remember having a similar issue a long time ago. If I remember
correctly, the culprit was a bad parametrization of the Langevin piston.
Maybe you should specified how the pressure is controlled, as well as how
you managed the center of mass motions in you dynamics.
Nicolas
Well the bilayer
it on Yahoo! Local
http://in.local.yahoo.com/
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Dear all
I am doing simulation of Dna-protein complex with using amber tools
with gromacs -4.0.3 . For this a/c to ffamber99.rtp file I have made lot of
changes in .pdb file after that pdb2gmx starts working but it give to
many warnings. like-
Warning: Long Bond (291-293 = 0.86645 nm)
Dear all,
I am experiencing some trouble with a small molecule containing a C-C
triple bond, using a topology built by PRODRG beta. I intend to use
ffG43a2, with a contraint on all bond lengths.
Energy minization does not converge, as forces on the atoms involved in
the bond seem to oscillate
Well .. I will rerun the simulations. setting this would do it, right:
comm_grps = POPC Solvent
where popc and solvent are the 2 groups ?
--
Maria G.
Technical University of Denmark
Copenhagen
___
gmx-users mailing listgmx-users@gromacs.org
nitu sharma wrote:
Dear all
You've broken something badly, like put the PDB information in columns
of the wrong width.
Mark
I am doing simulation of Dna-protein complex with using amber
tools with gromacs -4.0.3 . For this a/c to ffamber99.rtp file I have
made lot of changes in
nitu sharma wrote:
Dear all
I am doing simulation of Dna-protein complex with using amber
tools with gromacs -4.0.3 . For this a/c to ffamber99.rtp file I have
made lot of changes in .pdb file after that pdb2gmx starts working
but it give to many warnings. like-
Please consult
You may not want to delete those molecules. It will be interesting to see,
whether they stay or leave throughout
the MD simulation after some time. My experience with the Sybyl software was
that after some energy minimization (thus removing large forces that could have
repelled the waters out
Maybe this previous post will be of some use:
http://lists.gromacs.org/pipermail/gmx-users/2009-May/042068.html
-Justin
Alexander Bujotzek wrote:
Dear all,
I am experiencing some trouble with a small molecule containing a C-C
triple bond, using a topology built by PRODRG beta. I intend to
I would first check that the COM motion ... before reruning! You might
endup
with the same problem if this is not the issue!
On Jul 3, 2009, at 3:26 PM, maria goranovic wrote:
Well .. I will rerun the simulations. setting this would do it, right:
comm_grps = POPC Solvent
where popc and
Hello,
I'm getting problems to simulate amorphous silica with potentials I made
myself : table_Si_Si.xvg, table_Si_O.xvg, table_O_O.xvg and table.xvg
(which should not be used as all the possible non-bonded interactions
are given in the three previous tables).
The generation of the topology file
Hi guys, i'm working on binding energy of two proteins. I will try to use
thermidynamic integration, but i'm afraid that this will take long time of
computing, and I just reading and learning about TI or other methods for
free energy calculation, so this will be a long time project
However, while
Felipe Villanelo wrote:
Hi guys, i'm working on binding energy of two proteins. I will try to
use thermidynamic integration, but i'm afraid that this will take long
time of computing, and I just reading and learning about TI or other
methods for free energy calculation, so this will be a long
David Waroquiers wrote:
Hello,
I'm getting problems to simulate amorphous silica with potentials I made
myself : table_Si_Si.xvg, table_Si_O.xvg, table_O_O.xvg and table.xvg
(which should not be used as all the possible non-bonded interactions
are given in the three previous tables).
The
Dear gmx users,
Through the manual, I learn of that both pdb2gmx and protonate can add H
atoms according to the hdb files. About it, I have some puzzles as follows:
Are the two programs equivalent in adding H atoms? If it is yes, why bother
to develop another program? It seems that
wuxiao wrote:
Dear gmx users, Through the manual, I learn of that both pdb2gmx and
protonate can add H atoms according to the hdb files. About it, I have some
puzzles as follows: Are the two programs equivalent in adding H atoms? If it
is yes, why bother to develop another program? It seems
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